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The hMRI-toolbox is an easy-to-use open-source and flexible tool, for qMRI data handling and processing. It allows the estimation of high-quality multi-parameter qMRI maps (longitudinal and effective transverse relaxation rates R1 and R2*, proton density PD and magnetisation transfer MT saturation) (Weiskopf et al. 2008 & 2013), followed by spatial registration in common space for statistical analysis (Draganski et al. 2011).
Embedded in the Statistical Parametric Mapping (SPM) framework, it can be readily combined with existing SPM toolboxes for estimating diffusion MRI parameter maps, and it benefits from the extensive range of established SPM tools for high-accuracy spatial registration and statistical inferences.
The qMRI maps generated by the toolbox can be used for quantitative parameter analysis and accurate delineation of subcortical brain structures. They are key input parameters for biophysical models designed to estimate tissue microstructure properties such as the MR g-ratio and to derive standard and novel MRI biomarkers (Mohammadi et al. 2015). The hMRI toolbox is therefore the first step towards in vivo histology using MRI (hMRI) and is being extended further in this direction.
The flexible and modular nature of the toolbox makes it usable for a wide range of data types, from the full MPM protocol to subsets of it, including e.g. single contrast echo trains for mapping R2* or variable flip angle data for R1 and PD mapping using multi-echo or single-echo data. The spatial processing part of the toolbox can be applied to any set of rotationally-invariant qMRI maps, including diffusion MRI scalar parameter maps as well as the standard (R1, PD, MT and R2*) MPM maps.
For a reference on the scientific background, methods and concepts please use the hMRI-toolbox paper and cite it when publishing results compiled with the hMRI-toolbox.
This wiki is a collection of documentation and information about using the hMRI-toolbox. It is an on-going project that will be updated regularly.
Please do not print these pages. This online Wiki is meant to be browsed online!!
GET STARTED
Instructions to install the toolbox, examples for setting up the acquisition protocol.
TOOLBOX DEVELOPMENT
Description of the development process and guidelines for developers.
JSON METADATA AND DICOM IMPORT
DICOM to NIFTI conversion retrieving the whole DICOM header, tools for metadata handling (get, set and search tools), to keep track of acquisition and processing parameters at each step of the process.
AUTO-REORIENT
A simple tool to reorient all images towards the MNI space prior to map creation and data processing.
MAP CREATION
Tools to create quantitative and semi-quantitative R1, R2*, MT and PD maps.
DENOISING
Provides different methods to denoise raw/processed MRI images.
PROCESSING
Spatial and statistical processing of the quantitative and semi-quantitative maps.
QUIQI
A method that accounts for the degradation of data quality due to motion in the analysis of MRI data.
DEFAULTS & CUSTOMIZATION
Description of the default acquisition and processing parameters provided with the toolbox,
how to customise them and when!
TIPS & TRICKS FOR PROCESSING AND DEBUGGING
Description of the tools available to automatise data processing and control results quality.
Guidelines and good practices to make sure your data are processed as expected, with the help of information stored in the metadata associated to the images & maps and in the parameters and messages log files.
BIDS compatibility
Documentation of the latest status of compatibility of the hMRI toolbox with the qMRI-BIDS standard for organising brain imaging data.
DEVELOP & CONTRIBUTE
Contributing to the hMRI-toolbox can be done in many ways and at many levels, from users to experienced developers, from using the mailing list to implement a new feature.
RELEASES & VERSIONING
Information about the release process, the existing releases and related changes.
DEMO DATASET
A demo dataset is available for download and used in the tutorial and examples.
HELP
A list of help information from each and every script in the toolbox.
REFERENCES
Bibliographical references of interest for the hMRI toolbox.